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Friday, October 20, 2017

Finngolians #2

The mad scientists are at it again. The quote below is from an American Society of Human Genetics (ASHG) talk abstract. For the whole thing see here. Now, as I've pointed out on this blog before, Finns do not have Buryat or Mongolian ancestry, or anything even closely related dating to the Middle Ages. What they do have is some sort of Siberian admixture, which has been poorly characterized to date, but is probably associated with archaeologically attested population movements across northern Eurasia during the metal ages.

We identified significant gene flow from the Buryats to the Finnish which was predicted to be occurred in 1,228 (±87) year. Moreover, 13.38% of Buryat admixture was predicted in the Finnish genome.

This sort of nonsense should never be let through peer review anywhere. It makes the ASHG and indeed population genetics look like a total joke. In fact, imagine if such sloppy inferences from population genetics are allowed to influence medical genetics work. Someone might eventually get hurt.
See also...
Finngolians #1R1a and R1b from an early Mongolian tomb

Buryat males carry 18.4% of N-F4205 formed 4500 ybp, TMRCA 3000 ybp. When we get 3 kya old N-F4205 we get an idea of the area of origin of this N branch which belongs to the same successful Bronze Age N-L1026 branch which is widespread in Northern Eurasia from Northeast Europe to Northeast Asia.

These two strains of ancestry (Neolithic/Mesolithic Central Siberia and Bronze Age Volga Ural) are also visible in Buryats in the admixture analysis: Figure S-1 (https://www.biorxiv.org/content/early/2014/07/30/005850.figures-only). Buryats seem to have c. 5-8 % of Central Siberian ancestry which probably made its way to Fennoscandia before the metal ages. Moreover, Buryats seem to have some Bronze Age Volga Uralic ancestry.

I'd need higher coverage samples to confirm that find, but in any case, to propose a Middle Ages date for the eastern introgression in Finns, and Buryats as the source, is not even controversial, it's just sloppy work.

Sorry for the off topic question, but does anyone know anything about DNA preservation? My mom is going to pass in the next day or two and I was thinking of looking into something like Securigene, though I need to see what options they have other than a blood sample (leukemia and a bone marrow transplant mean her blood is all the donors or the cancer).

Anyone know anything about this? How much they preserve and how well? Enough to get a high coverage full genome at some point?

Just looking to preserve at least something of what makes her unique and special.

@Davidski ”Middle Ages date for the eastern introgression in Finns, and Buryats as the source”

Yes, if one takes a look at Wikipedia, one sees what happened in Buryatia in the middle Ages:

“The Buryat people are descended from various Siberian and Mongol peoples that inhabited the Lake Baikal Region including Kurykans, who are also the ancestors of the Siberian Turkic speaking Yakuts. Then in the 13th century the Mongolians came up and subjugated the various Buryat tribes (Bulgachin, Kheremchin) around Lake Baikal. The name "Buriyad" is mentioned as one of the forest people for the first time in The Secret History of the Mongols (possibly 1240). It says Jochi, the eldest son of Genghis Khan, marched north to subjugate the Buryats in 1207. The Buryats lived along the Angara River and its tributaries at this time."

"The ancestors of most modern Buryats were speaking a variety of Turkic-Tungusic dialects at that time. In addition to genuine Buryat-Mongol tribes (Bulagad, Khori, Ekhired, Khongoodor) that merged with the Buryats, the Buryats also assimilated other groups, including some Oirats, the Khalkha, Tungus (Evenks) and others."

You would expect a geneticist to at least consult Wikipedia if not anything else on the history of the population under analysis.

It is ridiculous if they really propose that due to the Mongol invasion of Buryatia there was an emigration of Buryats to Finland.

While it is likely that what the authors detect is ancient Siberian admixture rather than "more recent" Mongolian admixture, without knowing their full methodology I am not sure that the tirade against the authors is warranted given huge gaping holes in population genetics of more "recent" history (past couple thousand years).

There remain enormously open questions regarding *known* Turkic+Mongolian migrations, and exactly how those migrations contributed to the ethnogenesis of even the Westernmost population speaking an Altaic language (e.g. Anatolian Turks). It seems this should have been a far easier problem to tackle than one concerning even more North-Westerly populations who do not speak an Altaic language at all (yeah, after the Uralic-Altaic "split"). Part of the complication may be due to the pre-existing complexity of the Anatolian landscape prior to the Selcuks entering Anatolia, while the other major part is due to the fact that no modern North/Central Asian population may accurately represent the East-to-West migrant Turks a millennium ago. But, both of these problems are coupled: Without understanding the nature of the migrations, it is difficult to understand the "autochthonous" Anatolian landscape circa 1000 AD (approximation given date of Malazgirt battle) given that much of that heritage is preserved in the presently admixed Anatolian Turkish population.

The English archaeologist Ramsay visiting my father's village a century ago referred to my great-great grandfather and his people as "Isaurian mountaineers". I could dismiss this as a Western romanticism of a more Easterly peoples were it not for the facts of my father's quite rare Y-haplogroup T1a occurs in relatively highest density amongst a specific Armenian Anatolian population combined with our recently discovered Armenian fourth-cousins. Not that I can express this so easily to some of my kind-of-fascist Pan-Turanist first cousins who are more focused around the fact that a few of us in my father's family can easily "pass" for ethnic Kazakhs, Kyrgyz, or Turkmen today -- something that is not contradicted by the non-negligible total NorthEast Asian autosomal component of my father's DNA, though his mtDNA hg H does not reveal this. Even my own mother, who simply could *not* "pass" for any North-Central Asian and whose closest non-immediate cousins are discovered to be various Kurdish families straight out of Iraqi Kurdistan (confirming what my maternal grandfather revealed to me, may he rest in Peace), has a quite significant NorthEast Asian autosomal component -- again, something unexpressed in her "pure" paternal/maternal lines (J2a1a/H5a).

On the other hand, my Iranian Azeri father-in-law, another Y-hg J person who hailed from beautiful mountains to the north of Iran -- may he also rest in Peace -- had completely negligible autosomal NorthEast Asian component -- although his mtDNA haplogroup A5b1b had only been found amongst Han Chinese thus far. One wonders how many more generations this A5b1b will remain in Iran as his only sister's only daughter has only sons...

While a sample space of one seems "meaningless" from a population genetics standpoint, it is important to remember that* People ultimately wish to infer genetic questions on the individual level via population genetics based analyses.* All kinds of claims have been made from sample size = 1 ancient remains already.* Even a sample space of one must be explained.

I repeat: For all of the studies done on human remains from eight thousand years ago, it is remarkable that we cannot say as much conclusively about far more recently known human populations (of which there are so so so many...).

As for myself and my own family, all that the DNA has uncovered is that -- no matter where our ancestors may have hailed, they certainly loved the mountains....

I'm pretty sure that I know what methods they used, and I'm also sure that there's no Mongolian admixture in Finland, otherwise it would've been detected by now with a variety of methods, including via uniparental markers.

Ryan, go to your mother, spend every minute with her and worry about DNA another time. Really. As someone who has been there I can tell you you're going to regret every minute you didn't spend with her.

I imagine the pre Uralic people of Finland as on the EHG/SHG continuum with Siberian admixture. There was also probably a large Corded Ware contribution during the BA. Then the Finno Ugric speakers would have arrived, who themselves may have looked like EHG or Corded Ware with Siberian admixture.

I'm guessing that post ANE Siberian arrived in Finland with Comb Ceramic culture around the late 6th millennium BCE. It seems to be the unifying factor for such ancestry in northern Eurasia, and it lines up well with the available archaeological and genetic evidence eg. Earliest comb ceramic pottery and earliest Yhg N found in Neolithic Northeast China, spreading across northern Eurasia from there.

If this is true, it would predate the Uralic expansion in the Bronze Age. Uralic itself would have expanded from a Comb Ceramic derived culture, but a different one from the Finnish pre Uralic comb ceramic.

The Urals lived in Siberia in the Taiga, as established by linguists and ethnographers. They arrived in Eastern Europe from Siberia, no earlier than the spread of Net Pottery Culture in the second Millennium BC, after there left representatives of the Fatyanovo culture due to the spread of the Taiga.

@Davidski "the precise time of arrival of post-ANE Siberian (ie. East Asian) admixture is still unknown."

If one takes a look at the Mesolithic mtDNA from West Siberia (4000-3000 BC), it looks very much modern Siberian and Native American: D4, Z1a, C4, C1, A10 + European U5a, U4 and U2e; and this area is not in East Asia but just east of the Urals, north of Kazakhstan close to Chelyabinsk and Tyumen.

It is not very audacious or far-fetched to imagine that this ancestry reached Fennoscandia by 3000 BC.

The original paper: V.I. Molodin et al., Human migrations in the southern region of the West Siberian Plain during the Bronze Age: Archaeological, palaeogenetic and anthropological data. Part of a wider book published by De Gruyter (2013)

Just discussing the CWC in Southern Finland with an acquaintance living in Finland. I shared this article with her: https://www.researchgate.net/profile/Kerkko_Nordqvist/publication/272710773_Distribution_of_corded_ware_in_the_areas_north_of_the_Gulf_of_Finland_-_An_update/links/551ac7e90cf2bb754077cc38/Distribution-of-corded-ware-in-the-areas-north-of-the-Gulf-of-Finland-An-update.pdf

Historical linguists that I've read think that Proto-Uralic spread as trade language in the Bronze Age. This accounts for some peculiarities of the structure of the language family, usually described as bush or comb, rather than the tree structure that results when languages spread by migration. The Uralic languages have pattern of adopting immediate-family kinship terms from substratum languages, but preserving Proto-Uralic term for more distant relatives and in-laws. This unusual (basic kinship terms are rarely borrowed), but it's consistent with Uralic-speaking traders marrying into local populations and adopting the local words for "son". "daughter", "brother", "sister", but preserving contacts with an extended-family network over a wider region, along with the Uralic terms for those relationships.

In this scenario, there's plenty of opportunity for Siberian admixture to show up in Uralic-speaking populations west of the Urals.

The Saami languages spread into northern Scandinavia, Finland and the Kola peninsula a bit later, in the iron-age, but following the same pattern. Based on place names, Saami languages, or Proto-Saami, appear to have historically been spoken further south, in the Finnish lake district. Saami languages being replaced in this region as Finnish-speaking farmers settled further north.

It's already known that Saami people have more Siberian admixture than other people in Scandinavia and Finland, and more than Scandinavian Hunter-Gatherers, who were presumably the source of the substratum of the Saami branch of the Uralic language family. When and how the Siberian admixture got there is unknown.

Most of the linguistics stuff in my comment comes from Ante Aikio, a Finnish historical linguist who's a native speaker of Northern Saami, and has done work with non-Uralic Siberian languages, as well as the Uralic language family. In interpreting these findings, we should probably look at previous linguistic research on the Uralic languages and previous genetic research in the region for context.

Everything I've said here recited from memory, and so it should be taken with a gain of salt.

"This unusual (basic kinship terms are rarely borrowed), but it's consistent with Uralic-speaking traders marrying into local populations and adopting the local words for "son". "daughter", "brother", "sister", but preserving contacts with an extended-family network over a wider region, along with the Uralic terms for those relationships."

I just looked up the origin of the Hungarian equivalents of your example words in a dictionary, and most of them have clear parallels in multiple Uralic languages (including ones that are not particularly close to Hungarian, like Finnish) or have evolved from Uralic roots. I am skeptical about your theory.

@Epoch - trust me I am. When she's asleep though or being tended to by nurses, that's when my mind latches on to these things.

@David - I gave them a call and it seems saliva doesn't work for someone having blood transfusions. She's had a stem cell transplant and has active leukemia so I guess anything where DNA from the blood can be involved as a no go. They suggested hair too.

Apparently they extract the DNA and separate the higher molecular weight fragments (mostly full chromosomes) and then dehydrate them for preservation. They figured 1-4 micrograms per capsule, so it should be enough for high coverage full sequencing eventually I would think?

I'm just not sure about the preservation though - not something I know anything about. It seems their samples are already being opened and sent to labs though so I guess it probably isn't terrible.

@Ryan Prevention Genetics does DNA Banking from saliva samples, and also postmortem blood and tissue samples. THey extract and dessicate the DNA and then store it, so there's no problems with preservation.

@Open - It's not hair samples so much as the follicle. I'm not sure tissue would be feasible given how much contamination it would have from her cancer, transfusions, and stem cell transplant. Hopefully this works.